GitHub for the SIB courses NGS - Genome variant analysis

Sentieon DNAseq

Sentieon DNAscope + Machine Learning Model

nRex: Germline and somatic single-nucleotide, short indel and structural variant calling

dv-trio provides a pipeline to call variants for a trio (father-mother-child) using DeepVariants [1]. Genomic Variant Calling Files (gVCFs) created by DeepVariants are then co_called together using GATK[2]. The resultant trio VCF is then post-processing with FamSeq[3] to eliminate mendelian errors.

Bioinformatics N' Stuff

Variant calling pipeline for germline enrichment NGS data

Some workflows I wrote for my phd projects

Scripts and containers to run the variant callers originally used in ONCOLINER

A CWL implementation of a modular GATK Variant Calling pipeline

GBS workflow using dDocent. This was designed to process GBS data from SEACONNECT project.

Variant calling of WGS datasets

Variant calling and PSMC workflows

Bash scripts for fastq to vcf pipeline, written for USyd Artemis HPC.

Miscellaneous pipelines for genomics computation analysis in a SGE HPC platform.

example genomics workflow for student training

Variant discovery pipeline

Workflow for biological validation of germline SNP and indel variant datasets.

Rapid comprehensive adaptive nanopore-sequencing of CNS tumours set-up and analysis pipeline

Complete Pipeline for RNA-seq data analysis: From FastQ to differntial gene expression to annotated Variations.